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This function identifies reactions in a metabolic network which transport metabolites accross the network boundary. Only the stroichiometric matrix is taken into account, so the identified reactions are basically those, having only one non-zero entry in their column of the stroichiometric matrix. In order to work, the network must be “open”, it must not contain boundary metabolites.
findExchReact(model)
If model
is of class '>modelorg
an object of class
'>reactId_Exch
is returned.
Otherwise, if model
is of class matrix
or
of class Matrix
, a logical vector is returned.
If element i
equals TRUE
, column i
of model
is an
exchange reaction. The function returns NULL
and gives a
warning, if no exchange reaction can be found.
A exchange reaction
Becker, S. A., Feist, A. M., Mo, M. L., Hannum, G., Palsson, B. <U+00D8>. and Herrgard, M. J. (2007) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2, 727--738.
Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., Kang, J., Hyduke, D. R. and Palsson, B. <U+00D8>. (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6, 1290--1307.
# NOT RUN {
data(Ec_core)
ex <- findExchReact(Ec_core)
# run FBA
opt <- optimizeProb(Ec_core)
# get flux distribution of exchange reactions
getFluxDist(opt, ex)
# }
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